Overview

• Total strains : 771
• Total SNVs before filter : 4433445
• Total SNVs after filter : 2633240
• Total indels before filter : 1435492
• Total indels after filter : 563932

Site-level quality filters

Number of variant sites removed by each filter

The left panel shows counts of variant sites removed by individual filter, and the right panel shows counts of variant sites removed by all combinations of filters.

Before filter stats

Variant count for each strain based on vcf containing all variant sites called by GATK (“soft-filter.vcf”).

Post filter stats

Variant count for each strain based on vcf containing only sites pass all filters (“hard-filter.vcf”).